KeyError: 'FRAMERATEHZ'

[istolarek]

I have aligned P4C2 pacbio data with blasr
sorted bam file with samtools and indexed with pbindex

after running ipdSummary I get the following error:

'FRAMERATEHZ'
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pbcommand/cli/core.py", line 136, in _pacbio_main_runner
return_code = exe_main_func(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 719, in args_runner
return kt.start()
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 393, in start
return self.run()
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 455, in run
ret = self._mainLoop()
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 626, in _mainLoop
self.loadSharedAlignmentSet(self.args.alignment_set)
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 602, in loadSharedAlignmentSet
referenceFastaFname=self.args.reference)
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2551, in init
super(AlignmentSet, self).init(*files, **kwargs)
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1876, in init
super(ReadSet, self).init(*files, **kwargs)
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 470, in init
self.updateCounts()
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2392, in updateCounts
self.assertIndexed()
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2193, in assertIndexed
self._assertIndexed((IndexedBamReader, CmpH5Reader))
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1833, in _assertIndexed
self._openFiles()
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1953, in _openFiles
resource = IndexedBamReader(location)
File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 385, in init
super(IndexedBamReader, self).init(fname, referenceFastaFname)
File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 199, in init
self._loadReadGroupInfo()
File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 116, in _loadReadGroupInfo
rgFrameRate = ds["FRAMERATEHZ"]
KeyError: 'FRAMERATEHZ'
2019-03-12 09:32:30,684 [ERROR] 'FRAMERATEHZ'
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pbcommand/cli/core.py", line 136, in _pacbio_main_runner
return_code = exe_main_func(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 719, in args_runner
return kt.start()
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 393, in start
return self.run()
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 455, in run
ret = self._mainLoop()
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 626, in _mainLoop
self.loadSharedAlignmentSet(self.args.alignment_set)
File "/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py", line 602, in loadSharedAlignmentSet
referenceFastaFname=self.args.reference)
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2551, in init
super(AlignmentSet, self).init(*files, **kwargs)
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1876, in init
super(ReadSet, self).init(*files, **kwargs)
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 470, in init
self.updateCounts()
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2392, in updateCounts
self.assertIndexed()
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 2193, in assertIndexed
self._assertIndexed((IndexedBamReader, CmpH5Reader))
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1833, in _assertIndexed
self._openFiles()
File "/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py", line 1953, in _openFiles
resource = IndexedBamReader(location)
File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 385, in init
super(IndexedBamReader, self).init(fname, referenceFastaFname)
File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 199, in init
self._loadReadGroupInfo()
File "/usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py", line 116, in _loadReadGroupInfo
rgFrameRate = ds["FRAMERATEHZ"]
KeyError: 'FRAMERATEHZ'

[weedcentipede]

For correcting this error you have to extract .bam file from .bax.h5 files (please refer to bax2bam), then you could use blasr (There other programs to do this) to align the reads against a reference with the previous extracted bam as input reads.

For further info see issue #58